PDBTools.jl v3.24.2 Benchmark

Software Versions

Hardware

Benchmarks were executed on a desktop computer with the following specifications:

• CPU: 13th Gen Intel Core i7-13700KF
• RAM: 32 GB
• GPU: NVIDIA GeForce RTX 4060 Ti
• Storage: Kingston NV2 NVMe SSD
• Network: Realtek RTL8125 2.5GbE

All benchmarks were run single-threaded. VMD is the only package that uses the GPU in these computations.

Methodology

• Reported times are the mean of three consecutive runs.
• For PDBTools.jl, one warm-up run was performed before timing to exclude Julia just-in-time (JIT) compilation overhead.
• Unless otherwise stated, timings exclude file reading, atom selection, and output writing.
  • GROMACS was the only exception, because these steps could not be separated from the command-line workflow.
  • For VMD, the file-opening overhead was estimated from the loading time of a single-atom PDB file and subtracted from the reported times.

Benchmark Systems

• Structures were obtained from the Protein Data Bank and contained only protein atoms.
• The first 11 systems were protein structures; the remaining nine were viral capsid structures.
• No periodic boundary conditions were used.

Analysis Parameters

For hydrogen-bond analysis, protein–water hydrogen bonds were analyzed.

References

• Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J Mol Graph 1996, 14 (1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
• Abraham, M. J. et al. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX 2015, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
• Gowers, R. et al. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the Python in Science Conference; SciPy, 2016; pp 98–105. https://doi.org/10.25080/majora-629e541a-00e
• Campbell, M. J. RustSASA: A Rust Crate for Accelerated Solvent Accessible Surface Area Calculations. J. Open Source Softw. 2026, 11 (117), 9537. https://doi.org/10.21105/joss.09537